5afa332cc12c75f441ffaf7fa2d9a219ec1f219b
chmalee
  Fri Nov 13 10:22:20 2020 -0800
Remove the superfluous fields 'Reference Seq' and 'Variant Seq' from the genome in a bottle sv track, refs #24349

diff --git src/hg/utils/otto/dbVar/processNstd175.py src/hg/utils/otto/dbVar/processNstd175.py
index ba46e3e..f7bca9c 100755
--- src/hg/utils/otto/dbVar/processNstd175.py
+++ src/hg/utils/otto/dbVar/processNstd175.py
@@ -1,29 +1,29 @@
 #!/usr/bin/env python3
 
 """
 Read GVF lines from stdin and write bed9+ lines to stdout
 """
 
 import os,sys,re
 import argparse
 
 bed9Fields = ["chrom", "chromStart", "chromEnd", "name", "score", "strand", "thickStart",
     "thickEnd", "itemRgb"]
 
 # the following list of fields may not exist for every record in the input file
-extraFieldList = ["Size", "Variant Type", "Variant Region", "Link to dbVar", "Sample Name", "Sampleset Name", "Phenotype", "Variant Seq", "Reference Seq"]
+extraFieldList = ["Size", "Variant Type", "Variant Region", "Link to dbVar", "Sample Name", "Sampleset Name", "Phenotype"]
 
 bedLines = {}
 chromLift = {}
 
 def setupCommandLine():
     parser = argparse.ArgumentParser(description="Read GVF lines from infile and transform to bed9+",
         add_help=True, usage = "%(prog)s [options]")
     parser.add_argument("infile", action="store", default=None, help="Input GVF file from which to read input, use 'stdin' to read from default stdin")
     parser.add_argument("liftFile", action="store", default=None, help="liftUp file for converting chrom names to UCSC style names")
     args = parser.parse_args()
     return args
 
 def parseLiftFile(fname):
     global chromLift
     with open(fname) as f:
@@ -65,31 +65,31 @@
         for field in fields:
             try:
                 if type(bed[field]) is list:
                     finalBed.append(", ".join(bed[field]))
                 else:
                     finalBed.append(str(bed[field]))
             except KeyError: # some of the extra fields won't exist for every record
                 finalBed.append("")
         print("\t".join(finalBed))
 
 def processExtraFields(extraFields):
     """Special processing of the GVF extra fields"""
     ret = {}
     for key in extraFields:
         val = extraFields[key]
-        if key == "ID" or key == "Name":
+        if key == "ID" or key == "Name" or key == "Variant Seq" or key == "Reference Seq":
             continue
         elif key == "Dbxref":
             splitxrefs = val.split(',')
             if len(splitxrefs) > 1:
                 sys.stderr.write("Error: more dbXref fields this release:\n")
                 sys.stderr.write("%s\n" % (extraFields))
                 sys.stderr.write("stopping\n")
                 sys.exit(1)
             else:
                 val = "https://" + val[4:]
                 ret["Link to dbVar"] = val
         elif key == "Parent":
             ret["Variant Region"] = val
         else:
             ret[key] = val